The Kai, spiritual leader of Bajor, exercised a great deal of political influence over the Provisional Government. Disputes between the Kai and the First Minister of the government, while rare, could be extremely divisive. While it was not forbidden for the Kai to serve as First Minister, such concentration of power was discouraged. The Kai was permitted to engage in foreign policy, including negotiating and signing treaties on behalf of Bajor, in consultation with the secular authorities. (DS9: "Emissary", "The Collaborator", "Life Support", "Shakaar", "Rapture", "In the Cards")

The Emissary, Benjamin Sisko, also had significant clout in the Provisional Government. Ministers sought his advice on political programs and schemes. Any measures endorsed by the Emissary were likely to pass the Council of Ministers. (DS9: "Shattered Mirror", "Call to Arms")

Further actions taken that year included the release of all Bajorans imprisoned for killing Cardassians during the Occupation and the enforcement of new building codes. (DS9: "A Man Alone", "Dax")

With the Federation's help, the Bajoran government began attempts to perform a massive energy transfer by tapping the molten core of its fifth moon, Jeraddo. Minister Toran was in charge of the energy project and to ensure that the moon's occupants were evacuated. Toran refused to hold up progress for three stubborn hold-outs, Mullibok, Baltrim and Keena, and forced Kira Nerys to remove the residents. She did so under protest. (DS9: "Progress")

When Aamin Marritza was arrested aboard Deep Space 9, and evidence of his presence at Gallitep was discovered, Minister of State Kaval congratulated Sisko for imprisoning Marritza, telling him he had performed a "special service" for Bajor. He refused to listen to Sisko's argument that Starfleet did not have grounds for holding the Cardassian, bluntly stating that "we will have him". He later placed Kira Nerys in charge of the investigation. (DS9: "Duet")

By early 2370, the Provisional Government was becoming increasingly unpopular. Its members were seen as political opportunists and its decision-making was hampered by in-fighting. With the death of the Kai, Bajor was left without a strong central authority. Civil strife ensued, with factional and religious tensions brought to the surface. In this environment, the xenophobic Alliance for Global Unity emerged as a threat to the survival of the Provisional Government. Unbeknownst to the Chamber of Ministers, the Circle was led by Minister Jaro Essa, who saw an opportunity to advance his own political ambitions.

Jaro perceived a threat to his rise to power, in the popularity of the war hero Li Nalas, recently freed from a labor camp on Cardassia IV. Jaro dealt with it by transferring MajorKira Nerys to a surface post, and assigning Li to DS9. Without Li's unifying influence, riots erupted across the planet. Disgruntled Bajorans angrily demanded a new government that could stand on its own. Armed with weapons purchased from Kressari traders, the Circle clashed with Bajoran Militia forces with increasing frequency. The Provisional Government was forced to deploy troops in Bajor's capital to put down unrest. However, the Militia was unable to stop the Circle; each potential conflict led to a further withdrawal.

Minister Jaro conspires with Vedek Winn

Jaro soon attracted support from Bajoran religious and military leaders, including VedekWinn and GeneralKrim. The coup was only foiled when Major Kira and Jadzia Dax arrived on Bajor with recently uncovered evidence regarding the Circle's weapon suppliers, in a shipping manifest. Cardassians, finding advantage in the Circle's disruption of Bajoran politics, had surreptitiously supplied the faction through intermediaries. The manifest, with a Cardassian Gul's thumb signature, convinced the Chamber of Ministers in time to avert the coup. (DS9: "The Homecoming", "The Circle", "The Siege")

Another major crisis in that year for the Provisional Government was the arrival of three million Skrreea refugees through the wormhole from the Gamma Quadrant. Their leader, Haneek, believing that Bajor was Kentanna, a promised land for the Skrreeans, petitioned the Provisional Government to allow them to settle on the planet. The Provisional Government considered Haneek's request, but in the end denied the Skrreea permission to immigrate, noting that it was having difficulty fixing the planet's existing problems. (DS9: "Sanctuary")

That same year, the Bajoran government expressed concern to Benjamin Sisko about Elim Garak's presence on Deep Space 9. Some Ministers in the government called for Garak's removal from the station. Sisko felt that he had no choice but to agree to their request, unless he could show them how Garak might be useful to them. Sisko used that to persuade Garak to participate in a clandestine mission to rescue Kira Nerys from the Obsidian Order on Cardassia Prime. (DS9: "Second Skin")

In 2373, the Bajoran government successfully petitioned the Federation for membership. However, the Council of Ministers voted to delay their acceptance after CaptainBenjamin Sisko, having had a series of visions, warned that it was too soon to join – that doing so would destroy Bajor. Sisko was later confronted by AdmiralCharlie Whatley, who asked Sisko to contact the Chamber of Ministers and convince them that he was mistaken, but Sisko refused. (DS9: "Rapture")

Later that year, the Bajoran government declined to intervene when Hagath and his associates sold weapons within the Bajoran system. Hagath had sold weapons to the Bajoran Resistance, and it was felt that the Bajorans at least partially owed their freedom to Hagath and people like him. (DS9: "Business as Usual")

Later that year, the Provisional Government signed a nonaggression pact with the Dominion following its endorsement by the Emissary, who argued that it was Bajor's only chance of survival. With the Federation forced to abandon Deep Space 9, the station was occupied by Dominion and Cardassian forces, who were officially welcomed into Bajoran space by Major Kira on behalf of the Provisional Government. (DS9: "In the Cards", "Call to Arms")

In 2374, Major Kira went to the Council of Ministers, asking them to lodge a formal protest against the planned execution of Rom. However, Weyoun had previously informed Kira that any protest by the Bajoran government would fall on deaf ears. (DS9: "Favor the Bold")

It can be inferred that Bajor withdrew from the nonaggression pact with the Dominion following their withdrawal from Terok Nor after Operation Return, as several lines of dialoge throughout seasons six and seven imply that the Bajoran government formally joined the war. However, this was not directly established onscreen.

The Treaty of Bajor document, made for Deep Space Nine's final episode, identifies Bajor's government as the "Bajoran Republic" and as one of the five signatories of the treaty alongside the United Federation of Planets, Klingon Empire, Romulan Star Empire and the Founders of the Dominion.

The Bajoran Militia was the military arm of the Bajoran Provisional Government, originally made up of many former resistance fighters from the Occupation of Bajor.

Although ostensibly under the control of the Provisional Government, some members of the organization, such as GeneralKrim, supported the Alliance of Global Unity's unsuccessful coup attempt in 2370. After the Circle's attempt was defeated, Krim and the Militia confirmed their allegiance to the Provisional Government. (DS9: "The Circle", "The Siege")